The Regulatory Genome

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Author: Eric H. Davidson
Publisher: Elsevier
ISBN: 9780080455570
Size: 37.91 MB
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The Regulatory Genome by Eric H. Davidson

Original Title: The Regulatory Genome

Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market. The only book in the market that is solely devoted to the genomic regulatory code for animal development Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding Presents a comprehensive treatment of molecular control elements that determine the function of genes Provides a comparative treatment of development, based on principles rather than description of developmental processes Considers the evolutionary processes in terms of the structural properties of gene regulatory networks Includes 42 full-color descriptive figures and diagrams

Regulatory Genomics

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Author: Hon Wai Leong
Publisher: Imperial College Press
ISBN: 1848162529
Size: 75.17 MB
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Regulatory Genomics by Hon Wai Leong

Original Title: Regulatory Genomics

Research in the field of gene regulation is evolving rapidly in the ever-changing scientific environment. Advances in microarray techniques and comparative genomics have enabled more comprehensive studies of regulatory genomics. The study of genomic binding locations of transcription factors has enabled a more comprehensive modeling of regulatory networks. In addition, complete genomic sequences and comparison of numerous related species have demonstrated the conservation of non-coding DNA sequences, which often provide evidence for cis-regulatory binding sites. Systematic methods to decipher the regulatory mechanism are also crucial for corroborating these regulatory networks; key to these methods are motif discovery algorithms that can help predict cis-regulatory elements. These DNA-motif discovery programs are becoming more sophisticated and are beginning to leverage evidence from comparative genomics. These topics and more were discussed at the 3rd Annual RECOMB Workshop on Regulatory Genomics, which brought together more than 90 attendees and included about 22 excellent talks from leading researchers in the field. This proceedings volume contains ten selected, original manuscripts that were presented during the workshop.

Systems Biology And Regulatory Genomics

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Author: Eleazar Eskin
Publisher: Springer Science & Business Media
ISBN: 3540482938
Size: 55.26 MB
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Systems Biology And Regulatory Genomics by Eleazar Eskin

Original Title: Systems Biology And Regulatory Genomics

This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2005 satellite events: the First Annual Workshop on Systems Biology, RSB 2005 and the Second Annual Workshop on Regulatory Genomics, RRG 2005, held in San Diego, CA, USA in December 2005. It contains 21 revised full papers that address a broad variety of topics in systems biology and regulatory genomics.

Regulatory Genomics

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Author: Bogdan Tanasa
ISBN: 9781303457241
Size: 80.17 MB
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Regulatory Genomics by Bogdan Tanasa

Original Title: Regulatory Genomics

In the present dissertation, I integrate contemporary high-throughput sequencing (HT-seq) methods to characterize regulatory elements and transcriptional units in several biological systems in order to understand the molecular networks regulating the processes of gene expression. Our intense efforts contributed to several discoveries in biology, including a. the discovery of novel small RNA species that regulate mRNAs stability - the riRNAs, b. finding novel transcriptional units that regulate estrogen-dependent transcriptional events - the eRNAs, c. establishing the role of long noncoding RNAs in androgen-dependent gene expression - the lincRNAs PCGEM1 and PRNCR1, d. elucidating a novel epigenomics regulator - PHF8 as a H4K20me1 demethylase, e. characterizing a multifaceted transcrip- tional regulator - GPS2, f. identifying novel GWAS loci located in enhancers that carry disease susceptibility alleles. Chapter 1 reviews the current knowledge on genome regulatory elements, transcriptional units and chromatin architecture, and it describes 8 computational protocols that I have established in the laboratory for data analysis, together with their biological applications and methodological limitations. Chapter 2 details the use of HT-seq methods to characterize 2 novel transcriptional regulators (PHF8 and GPS2 ) that associate with promoters. Chapter 3 describes a novel small RNA species (riRNAs ), that derives from Alu retrotransposons and was bioin- formatically predicted to target the mRNAs. Chapter 4 describes the functions of enhancer RNAs in gene expression and chromatin interactions, by employ- ing GRO-seq and 3D-DSL methods. Chapter 5 describes 2 lincRNAs (PRNCR1, PCGEM1 ) that are over-expressed in prostate cancers and regulate tumor growth, by using ChIRP-seq and GRO-seq methods. Chapter 6 describes the biological functions of an enhancer in 9p21 gene desert, that carries genetic susceptibility to disease, and advances in 3D-DSL technology. I conclude with a section that summarizes these discoveries and outlines the potential areas of future research.

Genomic Control Process

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Author: Isabelle Peter
Publisher: Academic Press
ISBN: 0124047467
Size: 65.43 MB
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Genomic Control Process by Isabelle Peter

Original Title: Genomic Control Process

Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type Demonstrates the causal power of system-level understanding of genomic control process Conceptually organizes a constellation of complex and diverse biological phenomena Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome

World Congress Of Medical Physics And Biomedical Engineering 2006

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Author: Sun I. Kim
Publisher: Springer Science & Business Media
ISBN: 3540368396
Size: 38.86 MB
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World Congress Of Medical Physics And Biomedical Engineering 2006 by Sun I. Kim

Original Title: World Congress Of Medical Physics And Biomedical Engineering 2006

These proceedings of the World Congress 2006, the fourteenth conference in this series, offer a strong scientific program covering a wide range of issues and challenges which are currently present in Medical physics and Biomedical Engineering. About 2,500 peer reviewed contributions are presented in a six volume book, comprising 25 tracks, joint conferences and symposia, and including invited contributions from well known researchers in this field.

Animal Evolution

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Author: Maximilian J. Telford
Publisher: Oxford University Press
ISBN: 0199549427
Size: 32.80 MB
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Animal Evolution by Maximilian J. Telford

Original Title: Animal Evolution

Describing and understanding the evolution of the diversity of bodyplans is a major goal of evolutionary biology. Taking a modern, integrated approach to this question, a group of leading researchers describe how modern techniques and disciplines have been combined, resulting in a dramatic renaissance in the study of animal evolution.

Towards A Theory Of Development

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Author: Alessandro Minelli
Publisher: OUP Oxford
ISBN: 0191651184
Size: 25.59 MB
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Towards A Theory Of Development by Alessandro Minelli

Original Title: Towards A Theory Of Development

Is it possible to explain and predict the development of living things? What is development? Articulate answers to these seemingly innocuous questions are far from straightforward. To date, no systematic, targeted effort has been made to construct a unifying theory of development. This novel work offers a unique exploration of the foundations of ontogeny by asking how the development of living things should be understood. It explores the key concepts of developmental biology, asks whether general principles of development can be discovered, and examines the role of models and theories. The two editors (one a biologist with long interest in the theoretical aspects of his discipline, the other a philosopher of science who has mainly worked on biological systems) have assembled a team of leading contributors who are representative of the scientific and philosophical community within which a diversity of thoughts are growing, and out of which a theory of development may eventually emerge. They analyse a wealth of approaches to concepts, models and theories of development, such as gene regulatory networks, accounts based on systems biology and on physics of soft matter, the different articulations of evolution and development, symbiont-induced development, as well as the widely discussed concepts of positional information and morphogenetic field, the idea of a 'programme' of development and its critiques, and the long-standing opposition between preformationist and epigenetic conceptions of development. Towards a Theory of Development is primarily aimed at students and researchers in the fields of 'evo-devo', developmental biology, theoretical biology, systems biology, biophysics, and the philosophy of science.

Mutation Driven Evolution

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Author: Masatoshi Nei
Publisher: OUP Oxford
ISBN: 0191637823
Size: 47.37 MB
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Mutation Driven Evolution by Masatoshi Nei

Original Title: Mutation Driven Evolution

The purpose of this book is to present a new mechanistic theory of mutation-driven evolution based on recent advances in genomics and evolutionary developmental biology. The theory asserts, perhaps somewhat controversially, that the driving force behind evolution is mutation, with natural selection being of only secondary importance. The word 'mutation' is used to describe any kind of change in DNA such as nucleotide substitution, gene duplication/deletion, chromosomal change, and genome duplication. A brief history of the principal evolutionary theories (Darwinism, mutationism, neo-Darwinism, and neo-mutationism) that preceded the theory of mutation-driven evolution is also presented in the context of the last 150 years of research. However, the core of the book is concerned with recent studies of genomics and the molecular basis of phenotypic evolution, and their relevance to mutation-driven evolution. In contrast to neo-Darwinism, mutation-driven evolution is capable of explaining real examples of evolution such as the evolution of olfactory receptors, sex-determination in animals, and the general scheme of hybrid sterility. In this sense the theory proposed is more realistic than its predecessors, and gives a more logical explanation of various evolutionary events. Mutation-Driven Evolution is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of molecular evolution and population genetics. It assumes that the readers are acquainted with basic knowledge of genetics and molecular biology.

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